Contacts of the helix formed by residues 133 - 148 (chain D) in PDB entry 3G33
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 133 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D CYS* 4.2 0.7 - - - -
130D HIS 4.9 2.6 + - - -
131D ALA 4.0 2.4 + - - -
132D VAL* 1.3 77.8 - - - +
134D PRO* 1.3 75.9 - - - +
135D ARG* 3.9 11.4 + - - +
136D GLN* 3.0 43.3 + - - +
137D LEU* 3.3 8.2 + - - +
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Residues in contact with PRO 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLY* 5.0 1.8 - - - -
121D ILE* 3.4 26.7 - - + +
122D GLU* 5.6 5.8 - - + -
125D CYS* 3.5 22.6 - - - -
133D SER* 1.3 88.7 - - - +
135D ARG* 1.3 65.1 + - + +
137D LEU* 3.3 4.3 + - + -
138D ARG* 3.2 43.4 + - - +
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Residues in contact with ARG 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D SER* 3.1 10.9 - - - +
134D PRO* 1.3 82.5 - - + +
136D GLN* 1.3 62.9 + - + +
137D LEU 3.3 0.7 + - - -
138D ARG* 3.3 26.8 + - - +
139D ASP* 3.1 31.0 + - - +
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Residues in contact with GLN 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D LEU* 4.0 27.5 - - + +
131D ALA 3.8 5.4 + - - +
132D VAL* 3.5 12.5 - - + +
133D SER* 3.0 37.3 + - - +
135D ARG* 1.3 78.8 - - + +
137D LEU* 1.3 58.0 + - - +
139D ASP* 3.5 4.4 + - - -
140D TRP* 3.0 39.9 + - + +
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Residues in contact with LEU 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY 5.3 1.1 - - - -
101D LEU* 3.8 22.0 - - + -
104D ALA* 3.9 17.7 - - + -
105D VAL* 3.8 19.4 - - + +
108D LEU* 4.7 11.3 - - + +
121D ILE* 3.4 46.4 - - + +
124D LEU* 4.2 20.2 - - + -
125D CYS* 4.9 2.7 - - + +
132D VAL* 4.0 9.4 - - + -
133D SER 3.3 7.1 + - - +
134D PRO* 3.6 10.3 - - + +
135D ARG 3.2 0.8 - - - -
136D GLN* 1.3 77.3 - - - +
138D ARG* 1.3 64.3 + - - +
140D TRP 4.0 0.2 - - - -
141D GLU* 3.1 24.6 + - - +
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Residues in contact with ARG 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASN* 4.4 18.6 - - - +
47A GLY* 5.0 5.0 - - - -
48A GLY 5.2 4.3 + - - -
51A GLY* 3.9 6.9 - - - -
52A GLY* 2.5 55.2 - - - +
121D ILE* 3.8 0.2 - - + -
134D PRO* 3.2 37.3 + - - +
135D ARG* 3.3 23.7 + - - +
137D LEU* 1.3 78.8 - - - +
139D ASP* 1.3 65.9 + - - +
141D GLU* 3.4 18.2 + - - +
142D VAL* 3.5 13.9 + - - +
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Residues in contact with ASP 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASN* 5.6 4.2 + - - +
86A SER* 5.4 5.2 + - - -
135D ARG* 3.1 22.4 + - - +
136D GLN* 3.9 5.6 - - - +
138D ARG* 1.3 79.2 - - - +
140D TRP* 1.3 63.7 + - + +
142D VAL* 3.1 12.2 + - - +
143D LEU* 3.0 23.4 + - - +
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Residues in contact with TRP 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D TYR* 3.7 26.9 - + - -
94D THR* 5.1 5.8 - - - -
98D GLN* 3.6 43.3 - - + -
101D LEU* 3.2 33.5 - - + +
102D LEU* 4.3 28.7 - - + -
105D VAL* 3.6 17.9 - - + -
136D GLN* 3.0 33.0 + - + +
139D ASP* 1.3 79.9 - - + +
141D GLU* 1.3 59.9 + - - +
143D LEU* 3.5 27.5 - - + +
144D VAL* 2.9 40.4 + - + +
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Residues in contact with GLU 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLY 4.9 0.3 - - - +
53A GLY* 4.0 5.4 - - - -
54A LEU* 2.9 39.5 + - + +
59A VAL* 5.1 0.3 - - - +
105D VAL* 3.6 12.1 - - + +
108D LEU* 3.7 16.4 - - + +
109D LEU* 3.7 23.5 - - + +
112D LYS* 2.6 36.3 + - - +
137D LEU 3.1 19.2 + - - +
138D ARG* 3.5 10.6 - - - +
139D ASP 3.2 0.2 - - - -
140D TRP* 1.3 76.6 - - - +
142D VAL* 1.3 61.3 - - - +
144D VAL* 4.1 1.6 - - - +
145D LEU* 3.2 29.2 + - - +
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Residues in contact with VAL 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ASN* 4.7 6.7 - - - +
54A LEU* 4.4 17.7 - - + -
84A ALA* 3.7 25.7 - - + +
85A THR* 5.9 0.2 - - - -
92A ILE* 3.6 35.9 - - + -
138D ARG 3.5 15.5 - - - +
139D ASP* 3.1 9.1 + - - +
141D GLU* 1.3 73.6 - - - +
143D LEU* 1.3 64.5 + - - +
145D LEU* 3.6 7.6 + - - +
146D GLY* 3.2 19.4 + - - -
150D TRP* 5.6 2.7 - - + -
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Residues in contact with LEU 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D TYR* 3.8 23.6 - - + +
139D ASP 3.0 13.7 + - - +
140D TRP* 3.2 41.3 + - + +
142D VAL* 1.3 78.0 - - - +
144D VAL* 1.3 62.1 + - - +
146D GLY* 3.4 2.3 + - - -
147D LYS* 3.2 36.5 + - + +
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Residues in contact with VAL 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TYR* 5.2 0.2 - - + -
88D TYR* 4.1 21.1 - - + -
102D LEU* 3.8 23.6 - - + -
105D VAL* 3.6 20.2 - - + -
106D CYS* 4.9 10.3 - - - -
109D LEU* 3.9 15.5 - - + -
140D TRP* 2.9 28.4 + - + +
141D GLU 4.1 0.7 - - - +
143D LEU* 1.3 73.0 - - - +
145D LEU* 1.3 66.7 + - - +
147D LYS* 3.3 1.6 + - - +
148D LEU* 2.9 45.1 + - + +
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Residues in contact with LEU 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.4 33.2 - - + -
59A VAL* 4.3 6.3 - - + -
109D LEU* 4.0 16.2 - - + -
141D GLU 3.2 17.7 + - - +
142D VAL* 3.8 4.7 - - - +
144D VAL* 1.3 78.7 - - - +
146D GLY* 1.3 56.8 + - - +
148D LEU* 3.2 3.5 + - - -
149D LYS 2.8 8.3 + - - -
150D TRP* 2.6 76.6 + - + +
152D LEU* 3.2 37.9 - - + -
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Residues in contact with GLY 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ASP* 5.3 0.3 - - - +
82A VAL 4.6 8.9 - - - +
84A ALA* 6.1 3.1 - - - -
142D VAL 3.2 12.7 + - - -
143D LEU 3.9 2.2 - - - -
145D LEU* 1.3 79.0 - - - +
147D LYS* 1.3 57.9 + - - +
149D LYS* 3.1 21.8 + - - +
150D TRP* 4.0 11.6 - - - +
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Residues in contact with LYS 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D TYR* 3.8 23.3 - - + +
91D CYS* 4.4 15.4 + - - -
92D VAL* 3.6 32.9 - - + +
143D LEU* 3.2 29.3 + - + +
144D VAL 3.3 4.4 + - - +
146D GLY* 1.3 77.2 - - - +
148D LEU* 1.3 64.6 + - - +
149D LYS* 3.2 4.1 - - - +
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Residues in contact with LEU 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TYR* 3.9 26.2 - - + +
87D ARG* 3.6 43.8 + - + +
88D TYR* 3.8 15.7 - - + +
91D CYS* 5.7 0.7 - - - -
144D VAL* 2.9 36.2 + - + +
145D LEU 4.0 2.0 - - - +
147D LYS* 1.3 81.0 - - - +
149D LYS* 1.3 70.6 + - - +
150D TRP 3.1 0.7 - - - -
151D ASP* 2.9 18.7 + - - +
152D LEU* 3.7 31.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il